I never said "plucked out of time." What I meant, and evidently didn't convey clearly enough, was that the war was waged non-linearly, that it explicitly involved going back and rewriting past events to undo defeats, so we can't assume that just because we saw a given Time Lord alive at a given point in history, that means that event is still part of the post-Time-War history.
Remember "Genesis of the Daleks?" The Time Lords sending the Doctor back into Skaro's past with instructions to prevent the Daleks from ever being created in the first place? That episode is retroactively regarded as the opening salvo of the Great Time War, and similar tactics were probably used routinely by both sides once the war was in full gear. So yes, it does seem likely that many of the combatants were not merely killed, but erased entirely. That's only to be expected when you're talking about a time war.